Method for Cell Line Development

ABSTRACT

The present invention relates to an improved method for cell line development (CLD) which is generally applicable to production of any therapeutic protein that can be produced using mammalian Cell lines and in particular Chinese Hamster Ovary (CHO) cells. 
     The method combines site-directed integration (SDI), expression construct components improving the post-transcriptional processing of the gene of interest (GOI) and the introduction of a onetime pre-CLD host cell line selection workflow to generate a production competent cell line that can then be used in multiple CLD efforts using SDI from that point on.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser.No. 16/490,623, filed Sep. 3, 2019, which claims the priority benefit ofPCT/EP2018/054466, filed Feb. 23, 2018. The content of theseapplications is incorporated by reference herein.

FIELD OF THE INVENTION

The present invention relates to an improved method for cell linedevelopment which is generally applicable to production of anytherapeutic protein that can be produced using mammalian Cell lines andin particular Chinese Hamster Ovary (CHO) cells.

BACKGROUND OF THE INVENTION

During the latest 30 years recombinant protein therapeutics has evolvedfrom a novelty to a dominating position among marketed drugs.Recombinant production of therapeutic proteins has surpassed the 100billion S per year market volume and plays an important role in theglobal economy as well as in advanced medical care. The therapeuticprotein class includes replacement proteins (insulin, growth factors,cytokines and blood factors), vaccines (antigens, VLPs) and monoclonalantibodies. The by far dominating format is the monoclonal antibodies.Some of the recombinant proteins can be produced in simple microbialcells such as E. coli, but for more complex proteins including themonoclonal antibody class Chinese Hamster Ovary (CHO) cells is thedominating host for production [1]. The monoclonal antibody class isprojected to continue being the dominating format but with a largerheterogeneity in molecular structure within this class includingdifferent multi-specific formats, fusion proteins, alternative scaffoldsand antibody drug conjugates (ADCs). However, since most of theseformats will still require advanced protein processing capacity(including glycosylation, disulfide formation and advanced foldingmachinery) not offered by microbial cells, CHO will likely continue tobe the dominating production host for many years to come.

Increased knowledge about the molecular details underlying humandiseases has revealed a huge heterogeneity of main diagnoses. As anexample, breast cancer is no longer considered to be one disease butconsists of at least several 10s of sub-diagnoses. Hence, proteintherapeutics is becoming more targeted towards specific molecularmechanisms and will most likely be even more so in the future. Thus anincreased number of drugs are needed to enable treatment of wholepopulations displaying different variants of disease at the molecularlevel. At the same time there is an increasing pressure to decrease thecost of healthcare, including drugs. Major contributors to the cost oftherapeutic protein drugs are the long development time and frequentlate failure of drug candidates. One approach to mitigate the risk oflate failure and increase the development speed is to evaluate multipledrug candidates early for their developability potential (titer inintended production host, aggregation tendency, formulation stability,immunogenicity). For this to work the production of early proteinmaterial must be highly similar to the intended final process andrequire a minimum of time and effort. For complex protein therapeuticsthe final production is generally performed in a clonal CHO cell linecarrying the recombinant genes stably inserted into the genome by aprocess referred to as Cell Line Development (CLD).

Currently the mainstream approach to cell line development using e.g.CHO (Chinese hamster ovary) cells is to use random integration of genesof interest followed by (a) selection of cells having the GOI (gene ofinterest) integrated and (b) a massive screening of clones to findspecific clones with favorable production characteristics. The reasonswhy screening is needed is twofold (i) As a GOI is integrated randomlyinto the genome the resulting transcription level will be impacted byepigenetic regulation in the region of insertion. A clone having the GOIintegrated into one or several highly active and stable genomiclocations is needed. Typical cell lines generated generally containbetween 5-20 copies of the GOI. (ii) A clone adapted to the burden ofexpressing a foreign protein at very high levels and with maintainedgood growth characteristics is needed. However, a CHO host cell is, forexample, not a very competent secretor. Further, the CHO genome ishighly plastic. By introducing expression of foreign secreted proteinsat very high levels an evolutionary pressure towards increased foldingand secretory capacity is introduced. By screening many clones, cellsbetter adapted for high secretion can be found. The best randomintegration platforms today can yield high protein titers in arelatively short time period (˜3 months) albeit using a very resourceintensive workflow. Further, generated cell clones will be different atthe genetic and phenotypic level between different cell line developmentefforts. This makes early developability assessment to improveefficiency of development difficult and increases process developmentefforts.

One potentially major improvement is to utilize targeted integration(site-directed integration; SDI) of genes of interest. In such ascenario a pre-identified genomic location known to support high andstable transcription is used as a target destination for GOIs in all CLDefforts. Using intelligent combinations of pre-introduced sequences andvector designs, including the use of co-transfected nucleic acid enzymessuch as nucleases or recombinases, will facilitate targeted insertionand ensure that all cells in culture will contain correctly insertedGOIs and hence have a high transcription rate [2-4]. This willsignificantly reduce the number of clones in the screening campaign. Allclones will have the same relatively high transcription rate and henceall clones will also have an evolutionary pressure towards improvedhandling of the recombinant protein production burden. However, at leasttwo challenges remain (1) SDI generally only integrates a single copy ofthe GOI and hence the level of expression and evolutionary pressure isgenerally lower than what can be achieved using random integration and(2) one still need to find a clone that has undergone genetic changesadapting it to e.g. high secretion etc.

SDI ensures a similar level of transcription for both different clonesfollowing a specific transfection of a GOI and between differenttransfections, even using different GOIs. However, numerous changesexist at the genetic and phenotypic level between a typical host cellline lacking recombinant genes in its genome and the final productionclone selected during CLD [5]. These differences represent thetransformation towards an increased capacity to handle the metabolicburden of producing a foreign recombinant protein at very high levels.Changes will likely include an increased capacity for (i) amino acidsynthesis and tRNA charging (ii) protein folding and (iii) proteinsecretion together with an efficient basic metabolic phenotype. Findingthe clone having undergone the desired transformation generally requiressubstantial screening. The CHO genome is highly plastic and thisplasticity forms the engine for introducing variation for screening.However, it is highly likely that the evolutionary pressure of highrecombinant protein expression is needed as an inherent selection agentto guide and maintain accumulation of a large number of changesbeneficial for recombinant protein production (and avoid accumulation ofnegative changes) in a single clone.

Thus, to increase speed and enable highly parallel developabilityassessments, there exists a need of an improved method for cell linedevelopment that reduces the need for screening and generates moresimilar cells between campaigns.

SUMMARY OF THE INVENTION

The present invention provides an improved and novel method for cellline development. The method combines SDI, expression constructcomponents improving the post-transcriptional processing of the GOI andthe introduction of a onetime pre-CLD host cell line selection workflowto generate a production competent cell line that can then be used inmultiple CLD efforts using SDI from that point on.

In a first aspect the invention provides a method for creating amammalian cell bank for cell line development comprising the followingsteps:

-   -   (a) providing a recombinant mammalian cell comprising (i) a        genomic region that is transcriptionally active during        suspension culture of said recombinant cell in a serum free        culture medium (ii) a recombinant template DNA construct        integrated at said genomic region, said recombinant template DNA        construct having a region containing elements needed for        expression of a template protein of interest and one or several        sequence elements enabling excision of said template protein of        interest region from said template DNA construct and optionally        the simultaneous introduction of a region from a donor DNA        construct into said template DNA construct;    -   (b) based on said recombinant cell generating one or several        candidate cells or cell populations;    -   (c) measuring production traits of said generated candidate        cells or cell populations and selecting a top candidate cell or        cell population having improved characteristics for production        of said template protein of interest;    -   (d) optionally providing a donor DNA construct containing (1)        one or several sequences enabling the integration of a region        from said donor DNA construct into said template DNA        construct (2) said donor DNA region further containing one or        several sequence elements Q enabling the introduction of an        expression vector DNA construct into said donor DNA region;    -   (e) treating said top candidate cell or cell population with a        DNA processing enzyme excising said template protein of interest        coding region from said top candidate cell or cell population        and optionally simultaneously introducing said donor DNA region        by targeted integration into said top candidate cell or cell        population resulting in the creation of a receiving DNA        construct with one or several functional sequence elements Q        enabling the targeted introduction of said expression vector DNA        construct into said receiving DNA construct;    -   (f) selecting a final cell or cell population were all cells        have undergone correct modification only; and    -   (g) from said final cell or cell population creating a cell bank        for cell line development, wherein said expression vector DNA        construct comprises a region encoding a desired protein of        interest belonging to the same class as said template protein of        interest, and wherein expression of said desired protein of        interest is achieved by using an expression vector to introduce        said expression vector DNA construct into said receiving DNA        construct at said genomic region of a cell or cell population        derived from said cell bank.

The same class in respect of protein of interest and template proteinrefers to a group of proteins sharing a common sequence or structuralfeature. Examples of protein classes include antibodies of the sameclass (such as IgG1 antibodies), fusion proteins sharing at least oneconserved domain (such as FC-fusion proteins), or in general proteinssharing a conserved scaffold sequence were sequence variation isintroduced only at defined region.

In the above method preferably;

-   -   (a) said template DNA construct comprises in 5′ to 3′ sequence        order a first recombinase recognition sequence, such as an attP        or attB sequence, a first copy of a second recombinase        recognition sequence, such as a loxP sequence, a promoter less        selection marker gene and a region coding for a template protein        of interest in any order and orientation followed by an        additional copy of said second recombinase recognition sequence,        such as a second loxP sequence; and    -   b) the promoter driving said promoter less selection marker gene        can be placed upstream of said first recombinase recognition        sequence or between said first recombinase recognition sequence        and said first copy of said second recombinase recognition        sequence or downstream of said second copy of said second        recombinase recognition sequence; and    -   (c) said first and second recombinase recognition sequences act        as recognition sequences for different recombinases; and    -   (d) said receiving DNA construct is created by the introduction        of a vector coding for a recombinase with specificity for said        second recognition sequence, such as Cre, catalyzing excision of        the region being flanked by said second recombinase recognition        sequences and leaving only a single second recombinase        recognition sequence, such as a loxP sequence, downstream of        said first recombinase recognition sequence; and    -   (e) said final cell or cell population is selected based on lack        of selection marker activity and/or genetic characterization.

The candidate cell or cell populations may for example be generatedaccording to any of the following procedures:

-   -   (a) isolating clones from a culture of said recombinant cell or        cell population or descendants thereof; or    -   (b) isolating pools or clones after (1) different culture time        in a continuous culture format such as a perfusion culture        or (2) different number of individual cultures starting with        inoculation of a first culture using said recombinant cell or        cell population or descendants thereof and using a volume from a        finished culture to inoculate a next culture or (3) a        combination of (1) and (2); or    -   (c) performing targeted engineering by applying gene editing        methods to introduce, remove or modify genetic material in the        genome of said recombinant cell or cell population or        descendants thereof; or    -   (d) using an isolated clone from a culture of said recombinant        cell or cell population or descendants thereof to inoculate a        culture in procedure (b); or    -   (e) any combination of procedures (a) to (d).

Steps (a) to (c) above may be iterated in the following way prior tocreating said cell bank:

-   -   (1) in a next iteration the top candidate cell population from        previous step (c) is used as said recombinant mammalian cell in        step (a) after having exchanged said template DNA construct for        a modified template DNA construct having been modified to        provide increased expression potential compared to modified        template DNA constructs in earlier iterations; and    -   (2) repeating (a)-(c) n times.

In the above method the template protein of interest is coded by asingle gene of interest or two or more genes of interest.

In a preferred embodiment of the above method said receiving DNAconstruct is introduced into said genomic location in the following way:

-   -   (a) providing a receiving DNA construct introduction vector        comprising said receiving DNA construct flanked by two sequences        X′ and Y′ being homologous to two corresponding sequences X and        Y in a template DNA construct containing cell and wherein said        sequences X and Y are unique or rare in the genome of said        template DNA construct containing cell and flanking said        template DNA construct;    -   (b) defining a gene editing nuclease recognition sequence within        said template DNA construct being unique or rare in the genome        of said template DNA construct containing cell;    -   (c) a vector(s) coding for a gene editing nuclease, such as a        zinc finger nuclease/meganuclease/TALEN or a CRISPR/Cas9        combination, with specificity for said gene editing nuclease        sequence is introduced together with said receiving DNA        construct introduction vector into a cell or a population of        cells from said recombinant mammalian cell;    -   (d) said gene editing nuclease creating a double strand break at        said gene editing nuclease sequence catalyzing integration of        said receiving DNA construct by cellular DNA repair mechanisms        such as homologous recombination;    -   (e) cells having undergone correct introduction are selected via        the use of a selection marker and/or genetic characterization.

The mammalian host cell line is preferably a CHO cell line such as CHODG44, CHO Kl, CHO M, CHO—S or a CHO GS knockout cell line.

In a second aspect, the invention relates to a method for mammalian cellline development comprising the following steps:

-   -   (a) providing a cell or cell population from a mammalian cell        bank developed according to the method described above and        having (i) a version of said receiving DNA construct containing        a sequence z2 being unique or rare in the total genome sequence        of said cell or cell population (ii) two sequences X and Y        flanking said receiving DNA construct and being unique or rare        in the genome of said mammalian cell;    -   (b) providing a matching expression vector in the form of a        plasmid containing sequences X′ and Y being homologous to said        sequences X and Y and wherein said sequences X′ and Y′ flanks a        desired protein of interest coding region including promoter(s)        and a second selection marker coding region including        promoter(s;    -   (c) introducing vector(s) coding for a gene editing nuclease        with specificity for said sequence z2 together with said        expression vector into said cell or cell population and wherein        said gene editing nuclease is designed using any available        technology platform such as zinc finger nucleases,        meganucleases, TALENs or CRISPR/Cas9 designs;    -   (d) said genome editing nuclease generates a double strand break        at sequence z2 catalyzing exchange of the regions flanked by        said sequences X and Y in said receiving DNA construct and X′        and Y′ in said expression vector via cellular DNA repair        mechanisms;    -   (e) a cell or cells having undergone correct cassette exchange        only are selected via the use of selection marker(s) and/or        genetic characterization.

In an alternative the method for mammalian cell line developmentcomprises the following steps:

-   -   (a) providing a cell or cell population from a mammalian cell        bank developed according to the above described method and        having aversion of said receiving DNA construct comprising two        recombinase recognition sequences flanking a first selection        marker coding region and wherein said recombinase recognition        sequences are both of the same type such as a serine recombinase        type such as attP/attB or a tyrosine recombinase type such as        Lox, Rox or FRT;    -   (b) providing a matching expression vector in the form of a        plasmid containing two recombinase recognition sequences        flanking a desired protein of interest coding region and a        second selection marker coding region in any order and        orientation, and wherein said recombinase recognition sequences        in the expression vector are of the same type as and matching        said recombinase recognition sequences in said receiving DNA        construct;    -   (c) introducing said expression vector together with vector(s)        coding for a recombinase, and wherein said recombinase is of any        type matching said recombinase recognition sequences in said        receiving DNA construct and said expression vector such as one        selected from the group of PhiC31, Cre, Dre, or Flp;    -   (d) said recombinase catalyzes the exchange of the regions        flanked by said recognition sequences in said receiving DNA        construct and said expression vector;    -   (e) a cell or cells having undergone correct cassette exchange        only are selected via the use of selection marker(s) and/or        genetic characterization.

In a further alternative the method for mammalian cell line developmentcomprises the following steps:

-   -   (a) providing a cell or cell population from a mammalian cell        bank developed according to the above described method and        having a version of said receiving DNA construct comprising a        single recombinase recognition sequence followed by an optional        first selection marker coding region and wherein said        recombinase recognition sequence is of type such as a serine        recombinase type such as attP/attB or a tyrosine recombinase        type such as Lox, Rox or FRT;    -   (b) providing a matching expression vector in the form of a        plasmid containing a recombinase recognition sequence followed        by a desired protein of interest coding region and a second        selection marker coding region in any order, and wherein said        recombinase recognition sequence in the expression vector is of        the same type as and matching said recombinase recognition        sequence in said receiving DNA construct;    -   (c) introducing said expression vector together with vector(s)        coding for a recombinase, and wherein said recombinase is of any        type matching said recombinase recognition sequences in said        receiving DNA construct and said expression vector such as one        selected from the group of PhiC31, Cre, Dre, or Flp;    -   (d) said recombinase catalyzes the integration of said        expression vector at said recognition sequence in said receiving        DNA construct resulting in the presence of a functional region        for expression of said desired protein of interest; and    -   (e) a cell or cells having undergone correct integration of the        expression vector only are selected via the use of selection        marker(s) and/or genetic characterization.

In yet a further alternative the method for mammalian cell linedevelopment comprises the following steps:

-   -   (a) providing a cell or cell population from a mammalian cell        bank developed according to the above described method and        having a version of said receiving DNA construct containing in        5′ to 3′ sequence order (i) a 5′ to 3′ directional promoter, a        first recombinase recognition sequence such as attP or attB and        a second recombinase recognition sequence such as loxP, or (ii)        a first recombinase recognition sequence such as attP or attB, a        3′ to 5′ directional promoter and a second recombinase        recognition sequence such as loxP, or (iii) a first recombinase        recognition sequence such as attP or attB, a second recombinase        recognition sequence such as loxP and 3′ to 5′ directional        promoter, and wherein said first and second recombinase        recognition sequences act as recognition sequences for different        recombinases;    -   (b) providing a matching expression vector in the form of a        plasmid containing in clockwise sequence order (i) a recombinase        recognition sequence followed by a promoter less selection        marker gene and a desired protein of interest coding region        including promoters, or (ii) a promoter less anti clockwise        encoded selection marker gene, a recombinase recognition        sequence and a desired protein of interest coding region        including promoters, and wherein said recombinase recognition        sequences in the expression vector are of the same type as and        matching said recombinase recognition sequences in said        receiving DNA construct;    -   (c) introducing said expression vector together with vector(s)        coding for a recombinase, and wherein said recombinase is of any        type matching said recombinase recognition sequences in said        receiving DNA construct and said expression vector such as one        selected from the group of PhiC31, Cre, Dre, or Flp; and    -   (d) said recombinase catalyzes the targeted integration of said        expression vector into said receiving DNA construct; (e) a cell        or cells having undergone correct integration only are selected        via the use of selection marker(s) and/or genetic        characterization.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 a describes a general workflow for generating a host cell line C2with improved properties; FIG. 1 b describes a streamlined CLD workflowusing the host cell line C2 for expression of a protein of interest;

FIG. 2 is an alternative to FIG. 1 and describes generation of animproved cell line Cn+1 using an iterative workflow wherein theisolation/selection steps are repeated multiple times using a graduallyincreased expression load;

FIG. 3 describes generation of the improved cell C2 carrying a receivingDNA construct R using a recombinase (Rec-RS2) to excise a TGOI regionbeing flanked by reversible recombinase target sequences RS2;

FIG. 4 describes a specific embodiment of the iterative approachdescribed in FIG. 2 wherein a reversible recombinase (Rec-RS2) is usedfor both insertion and excision of TGOIs with increasing expression loadfor each iteration;

FIG. 5 describes cell line development using the cell C2 as generated inFIG. 3 and highlighting alternative designs possible dependent onpromoter and SM placement;

FIG. 6 describes one specific embodiment of the iterative approachdescribed in FIG. 2 wherein cassette exchange is utilized mediated by adouble strand break inducing site specific nuclease;

FIG. 7 describes modifying the template recombinant DNA construct T ofthe improved cell C1 to a cell C2 carrying a receiving recombinant DNAconstruct R being ready for Cell Line Development via the use of DoubleStrand Break Induced Homologous Recombination (Gene Editing);

FIG. 8 describes cell line development using different promoterplacements in an improved cell C2 carrying a cassette exchange designbased on two recombinase recognition sequences (RS); and

FIG. 9 describes cell line development using different promoterplacements in an improved cell C2 carrying a single recombinaserecognition sequences (RS).

DETAILED DESCRIPTION OF THE INVENTION

The invention will now be described more closely in association with theaccompanying drawings and some non-limiting Examples.

A unifying concept underlying the invention is the time limitedutilization of an actively expressed template protein of interest forguiding the transformation of an initial mammalian host cell line havinglimited production capacity for a certain class of proteins into a highproductivity host cell line that can be used for efficient production ofany desired proteins of interest using Site-Directed Integration methodsfor CLD and were the desired protein of interest belongs to the sameclass as the template protein of interest. The invention includesmethods enabling controlled removal of template protein of interestexpression before expression of a desired protein of interest isinitiated. Compared to potential methods using targeted engineeringmethods without the continuous expression of a template protein ofinterest to enable the desired transformation the current inventionoffers improvements in that the effects of single or multiple changescan be directly assessed using a protein indicative of the performancefor a desired class of proteins and that the expression conditions usedfor the template protein of interest (mRNA levels and mRNA design) canbe reproduced for any desired protein of interest.

In a preferred embodiment a key aspect of the invention is theopportunistic utilization of the inherent plasticity of the genome oftypical mammalian host cell lines, such as the CHO genome, as an enginefor generating epi-genetic and/or genetic changes enabling the desiredtransformation into a high productivity state and where the continuoushigh level expression of a template protein of interest during thetransformation is used as an inherent selection agent and/orphysiological state sensor directing and/or enabling detection ofaccumulation of positive changes leading towards the desired end goal.The potential for template protein of interest expression acting as aninherent selection agent is based on the fact that a high recombinantexpression load imposed on all cells will have an impact on theirviability and growth. Cells that do not handle the recombinantexpression load well are hypothesized (and this is generally accepted inthe field) to be subjected to stress responses (amino acid shortage,charged tRNA shortage, hold up of the ribosomal machinery of recombinantmRNAs, hold up of the folding machinery on recombinant proteins,build-up of soluble or aggregated forms of recombinant protein withincells) reducing viability and growth. Further, cells havinggenetic/epigenetic changes leading to an improved handling of therecombinant expression load are hypothesized to have a higher viabilityand growth. Hence, by culturing cells for many generations, farexceeding what is used in typical CLD workflows, a large diversity ofgenetic/epigenetic changes are sampled and enrichment of cells havingaccumulated multiple positive changes are hypothesized based on thisdirected evolution mechanism. An alternative way of screening through amassive diversity, far exceeding current scope in CLD workflows, is toutilize the template protein expression as a physiological state sensorand perform iterative stages of clone screening followed by periods ofculturing. Each state of culturing introduces new diversity anddiversity can also be increased above natural levels via the use ofepi-genetic de-regulators or means to increase mutation rates.

In a further preferred implementation the genome of the improved hostcell line is stabilized (“Frozen”) using targeted gene editing methods[8] following the desired transformation. Compared to potentialapproaches using targeted engineering only to achieve the desiredtransformation the current invention offers potential largeimprovements. As shown in comparison of host cell lines and producercell lines, generated using cell line development screening efforts, alarge number of more or less subtle differences rather than a fewdramatic differences exists between the low productivity and the highproductivity state [5]. Examples known in the art has also shown limitedsuccess using single or a few targeted changes only and typically suchchanges yield competitive performance first after being combined withchanges introduced using selection workflows (and hence the plasticityof genomes) following introduction of genes coding for a protein ofinterest [12]. Hence it is likely that a large number (10s to 100s) ofmore or less subtle changes spanning over many different cellularpathways are needed to transform for example a CHO cell to a highproductivity state. Further it is likely that different protein classeswill need at least partly different modifications for optimalperformance. To achieve such large numbers of changes and changes withsuch precision in their effect will be highly challenging usingtargeting engineering approaches. First the desired changes must beunderstood and this will likely include a combination of major screeningefforts and advanced systems biology modeling and even so combinatorialeffects might easily be missed. Secondly, generating clones having thecorrect set of multiple changes will require a range of gene editingtools and major selection and screening. The approach based on utilizingthe plasticity of host cell genomes during a pro-longed time perioddisclosed in the current invention offers a means to sculpture thecomplete genome to achieve the desired transformation without the needfor massive screening to understand and define the changes needed or theneed for a large range of costly genome editing reagents. Further, thepostulated cost and resource effectiveness of the proposed approachcould enable the generation of a range of host cell lines being adaptedfor the optimal production of different protein/biotherapeutic classesor even sub-groups with different characteristics (such as amino acidfrequencies) within a given class. Finally, the non-targeted sculpturingof the genome can be combined with specific targeted changes introducedby genome editing. Such changes could include modulation/control ofglycosylation, further boosting of specific parts of the secretionmachinery, introduction of machinery for non-natural amino acids,introduction of machinery for specific post translational proteinmodifications and the already mentioned changes for stabilizing thegenome of a host cell.

A typical limitation of SDI based CLD approaches utilizing a single copyof the GOI known in the art have been to reach high enough total proteintranslation rates. A typical cell line generated using randomintegration typically contains 5-20 copies of the GOI and hence gives ahigher total protein translation rate based on higher mRNA levels. Thesingle copy integration limits the maximum cell specific productivityobtainable using a specific recombinant gene construct design, but willalso reduce the evolutionary pressure imposed on cells and is likely tonegatively impact the selection of a high productivity phenotype as alower expression load limits the detection of high performing phenotypesin a heterogenic population as the best phenotypes capable of expressingthe protein well above the expression load cannot be distinguished frommedium performance phenotypes just coping with the expression load.Hence, an important feature of the invention is to ensure a recombinantgene construct design enabling highly efficient mRNA translation tocompensate for the lower mRNA levels or to use alternative promotersenabling increased mRNA levels from a single gene copy. In someembodiments this can be achieved by sequence designs promoting increasedribosome recruitment, increased translation initiation and optimizedspeed and minimized error rates in the translation elongation of thecoding region. In a preferred embodiment of the method of the inventionuse is made of translational enhancement elements (TEEs) [6] in the5′-UTR and RESCUE modification [7] of the coding region.

With the combined solution described above (a pre-selected improved hostcell line and improved translation and or promoters) competitive titersusing single copy GOI integration should be possible and since screeningof clones is expected to be at a minimum the time and resources neededfor a CLD campaign will be significantly reduced allowing cost savingsby shortened time to clinic and market. Since cells generated fromdifferent CLD efforts using different candidate constructs are expectedto be highly similar both at the genetic and phenotypic level it will bepossible to perform comparisons of developability traits(immunogenicity, protein titers, aggregation levels, proteinself-association, binding specificity, formulation stability etc.) foran increased number of protein candidates in each drug developmentprogram and with stable cell lines identical to ones used in finalproduction and without the data being corrupted by variation coming fromdifferences in the physiological state of cell lines. This can in turnenable even larger cost savings and efficiency increases in drugdevelopment by increasing the likelihood of success and reducing therates of late failures. In addition, by having control of the gene copynumber, other expression elements of the GOIs and having increasedcontrol over the expression stability of GOIs more ambitious andpro-longed screening of host cell clonal diversity can be performed withpotential to generate phenotypes with superior production traits for acertain protein class as compared to typical cell lines generated usingrandom integration approaches or SDI approaches with modest screeningknown in the art. Finally an improved host cell line generated using anyof the embodiments of the invention, potentially using significantefforts and resources, can be used for any desired number of CLD effortsusing different desired proteins of interest of a similar protein class.

A conceptual general workflow for generating such a host cell line withimproved properties can be found in FIG. 1 a . First, an initialmammalian cell (C) carrying a single copy of a template DNA construct T,containing a fully functional template gene of interest (TGOI), at adefined location in the genome (HS) is provided. This cell is then putthrough a selection workflow (S1) to isolate/select a cell (C1) withhighly increased capacity to produce the template protein of interest.The improved C1 cell will have a modified genome (G1) and/ortranscriptome compared to the original cell genome (G) and/ortranscriptome reflecting multiple accumulated changes in diversecellular pathways and processes which together give rise to a phenotypewith the improved expression capacity. In a following step the templateDNA construct (T) of the improved cell C1 is modified to create areceiving DNA construct (R) lacking the TGOI but containing sequences Qenabling targeted integration of a desired gene of interest (GOI) from amatching expression vector (EV). This can either be achieved via the useof a DNA modifying enzyme (I) in solitude cutting out the TGOIcontaining region from T or via the combined use of a DNA modifyingenzyme (I) and a donor DNA construct vector (DV). The resulting cell C2will contain a receiving DNA construct (R) carrying sequences Q enablingsite directed integration of a GOI. C2 can then be used in a streamlinedCLD workflow (FIG. 1 b ) in which C2 is contacted with an expressionvector (EV) containing a matching recombinant construct R′ enabling atargeted integration of a desired protein of interest gene byintroduction of R′ from EV with the aid of a DNA modifying enzyme withspecificity for Q (Q) to create a cell C3 maintaining the expressionphenotype and genome (G1) of C2 but now expressing the desired proteinof interest. The genomic location should preferably be a hot spotregion, meaning that it supports high transcription of introduced genesand that this transcription is stable over time and reproducible fordifferent genes and different culture conditions. Especially thetranscription activity should be high and stable using a serum freeculture medium and growth during suspension conditions. Hot spot regionscan be identified either via screening approaches, bioinformatics or acombination of these. The current invention builds on that a definedgenomic location has been selected and that the sequence of this genomicsite is known. The template DNA construct T contains a TGOI andoptionally gene(s) coding for selection marker(s) (SM(s)). Preferablythe TGOI design contains genetic elements either outside or inside thecoding sequence(s) providing a high level translation power for thecorresponding protein to maximize the expression load/potential. Suchelements can include strong promoters such as mCMV, hCMV or syntheticpromoters [13], 5′-UTR designs providing increased mRNA stability and/orincreased translation, 3′-UTR designs providing increased mRNA stabilityand/or increased translation, signal peptides providing improvedsecretion properties and optimized sequence stretches in coding regionsbased on synonymous codon changes. Preferentially, design of thesesequence elements are based on TEEs in the 5′-UTR andRESCUE-modification of the coding region [6, 7].

The generation of an improved cell can either be performed using asingle TGOI expression load as outlined in FIG. 1 or by an iterativeimprovement workflow in which the expression load is gradually increasedand intermittent improved cells are isolated after each increase inexpression load until a final improved cell is generated as outlined inFIG. 2 . In this workflow the first step improved cell carrying arecombinant DNA construct T enabling a first TGOI expression load iscontacted with exchange vector(s) enabling modification of T includingintroduction of a new template DNA construct T1enabling a second higherTGOI expression load. This in turn enables the selection of a secondstep improved cell. This gradual increase in expression load can berepeated any number of times until a final improved cell is generated.The expression load can be varied by using different promoter strengthsin different TGOI construct generations, by utilizing 5′-UTR and 3′-UTRvariants promoting different mRNA stability and/or translationalefficiency, by utilizing coding sequences promoting different mRNAstability and/or translational efficiency or by changing the TGOI copynumber between different generations. One specific embodiment of thisiterative approach is to utilize cassette exchange mediated by a doublestand break inducing site specific nuclease (Nz) as outlined in FIG. 6 .Here the template DNA construct T contains a sequence X at the 5′-end, asequence Y at the 3′-end and an internal sequence z. All sequences X, Yand z are unique or rare in the genome (G1) of cell C1. To exchange Tfor T1 the cell C1 is contacted with an exchange vector V carrying T1anda site specific nuclease (Nz) with specificity for z. T1 containsequences at the ends that are either identical to or highly similar tothe sequences X and Y in T. The site specific nuclease creates a doublestrand break at z catalyzing cassette exchange between T and T1 viahomologous recombination repair mechanisms using T1 as a repairtemplate. If additional cassette exchange reactions are planned T1should also contain a sequence z1 being unique or rare in the genome(G1) to enable cassette exchange using a second site specific nucleasewith specificity for z1. The site specific nuclease can be any type ofgene editing solution such as zinc finger nucleases, homingendonucleases, TALENs or CRISPR/Cas9 variants. An alternative to usinggene editing assisted homologous recombination for exchanging TGOIvariants is to utilize reversible recombinase systems, see FIG. 4 , suchas solutions based on Cre/loxP (RS2/Rec-RS2 in general terms) in which aTGOI variant (TGOIn) can be introduced at a loxP (RS2) sequence via theaid of the Cre recombinase (Rec-RS2) resulting in an introduced TGOIflanked by two loxP (RS2) sequences. Following isolation of an improvedcell the previous generation TGOI can be removed via the action of Cre(Rec-RS2) which re-creates the single loxP (RS2) sequence enablingintroduction of a new generation TGOI.

Two main approaches can be used to isolate an improved cell from aninitial TGOI carrying cell. The first approach utilizes the inherentplasticity of the genome of typical mammalian host cell lines used forrecombinant protein production. One embodiment of this approach togenerate an improved cell line with improved properties is to screenclones from a culture for a desired set of protein production traits andselect the top performing clone. Protein production traits could be, butare not limited to: template protein of interest production rate orculture titer, template protein of interest aggregation level, templateprotein of interest charge heterogeneity, template protein of interestsize heterogeneity, glycosylation site occupancy and glycosylationprofile for the template protein of interest, cell growthcharacteristics and cell metabolic characteristics, tertiary structureprofile for the template protein of interest, template protein ofinterest self-association tendency, DNA sequence profiles, mRNAprofiles, miRNA profiles, proteomic profiles and genomic stability ofcells. This can in principle be performed in analogy with current CLDscreening approaches used in the field. There initial screens of manyclones using simple parallel culture formats and a few measuredparameters such as titer and growth are followed by more extensivescreening, including protein quality attributes as described above, of alower amount of selected clones in more predictive culture formats suchas shake flasks or bioreactors.

A second embodiment is based on directed evolution of the cells viapro-longed culture of the cells with recombinant expression pressurepresent. The high recombinant expression load imposed on all cells willhave an impact on the viability and growth. Cells that do not handle therecombinant expression load well are hypothesized to be subjected tostress responses (amino acid shortage, charged tRNA shortage, hold up ofthe ribosomal machinery of recombinant mRNAs, hold up of the foldingmachinery on recombinant proteins, build-up of soluble or aggregatedforms of recombinant protein within cells) reducing viability andgrowth. Further, cells having genetic/epigenetic changes leading to animproved handling of the recombinant expression load are hypothesized tohave a higher viability and growth. Hence, by culturing cells for manygenerations, far exceeding what is used in typical CLD workflows, alarge diversity of genetic/epigenetic changes are sampled and enrichmentof cells having accumulated multiple positive changes are hypothesizedbased on this directed evolution mechanism.

Preferentially the TGOI codes for a template protein of interestrepresenting an important class of proteins such as IgG1 antibodies orFC-fusion proteins and preferentially a difficult to express protein ofthis class to promote isolation of the highest possible productioncompetency of the generated host cell line. Preferentially the cultureof the cells is performed using conditions highly similar to a platformprocess defined for production of protein for clinical phases orcommercial purposes to enable the adaptation through directed evolutionto be directly compatible with these conditions. This could for examplemean using a bioreactor fed-batch culture with defined culture medium,feed medium and process parameters. Pro-longed culture in this formatcould for example be achieved by inoculation of next generation culturesusing a fraction of the culture from the previous culture. Prolongedculture could also be achieved in a chemostat reactor or a perfusionculture, potentially repeated multiple times using seeding of cells froma previous culture stage. Preferentially a selection marker, such asNeomycin resistance, a DHFR gene or a GS gene, is used together withculture conditions that put a strong selection pressure for the presenceof an active selection marker. This could for example be the use of aneomycin resistance gene as selection marker and the use of neomycinduring culture.

Another potential selection marker design could utilize a geneticcircuit coupling cellular survival directly to expression of the TGOI.Such a genetic circuit could be based on non-native miRNAs binding bothto a sequence stretch of TGOI mRNA and a sequence stretch on a selectionmarker gene such as NeoR, GS or DHFR. This is to further ensure, inaddition to the use of a transcription hot spot region, that theexpression construct is not silenced during culture leading to theenrichment of cells that are not expressing the template protein ofinterest. This approach has the potential to generate superior proteinproduction clones as compared to approaches based on mere screening ofclones. Typically in screening approaches a first culture is performedto select a first set of clones from. Individual clones are cultured forassessment followed by a second selection of clones. This is repeated afew times. As genetic variants are removed early and a low number ofgenerations are allowed between selection steps a relatively low amountof genome variation is sampled using this approach. Using directedevolution and pro-longed culture for many generations keep all thegenetic variation and allows time for accumulation of rare modificationsand most importantly rare combinations of changes. Importantly, usingthis approach on a cell line lacking a TGOI would most certainly notlead to the same accumulation of positive protein production traits asmost such changes would not be favored without the evolutionary pressureof high recombinant expression load and would not be possible to detectwithout the presence of a TGOI. Directed evolution and screening canalso be combined and preferentially at least one final step includingscreening of production traits should be included. Intermediatescreening steps in a workflow based on directed evolution can be used tofurther ensure that the rare event of clones having managed to silencethe SM/TGOI does not lead to such cells being enriched in cultures. Ifthe workflow starts with a clone screening and selection step a range ofmedium to high performance clones should preferably be selected for around of culturing to ensure a large genetic diversity. Finally, a cloneor a pool of cells isolated from any of these workflows is used tocreate a master cell bank (MCB) of a final improved host cell line. Thefinal host cell line having accumulated genetic and/or epigeneticchanges compared to the initial host cell line and recombinant mammalianhost cell. In addition to the phenotypic diversity generated during cellgrowth, phenotypic diversity could also be artificially increasedbetween selection/screening rounds by use of chemicals such asepigenetic de-regulators or by radiation increasing mutation rates.

Besides utilizing the natural or artificially enhanced plasticity in thegenome to sample or promote random changes, a second approach based ontargeted engineering can also be used to generate the final host cellline for CLD. A cell (C) according to FIG. 1 a being subjected to adefined TGOI expression load is subjected to targeted changes to thegenome (G) via the use of genome editing enzymes (such as Zinc fingernucleases, meganucleases, TALENs, CRISPR/Cas9 variants) and recombinantnucleic acid donor constructs to knock-out genetic functionality or addnovel genetic functionality. After selection of cells having undergonecorrect/desired changes, the effect of these targeted changes isevaluated in follow up cultures to look at protein production traitssuch as those described above.

A range of different individual targeted changes can be evaluated andcells with targeted changes having positive effects on proteinproduction traits can then be subjected to an iterative approach addingand evaluating additional changes. This process can be repeated until afinal clone or cell pool with desired properties (based on theaccumulation of one or multiple targeted changes) can be isolated.Preferentially the evaluation of protein production traits is performedusing culture conditions highly similar to a platform process definedfor production of proteins for clinical phases or commercial purposes toenable a fit to these conditions. This could for example mean using abioreactor fed-batch culture with defined culture medium, feed mediumand process parameters. Compared to targeted engineering approachesapplied on host cell lines lacking a TGOI, the method according to thepresent invention enables several major advantages. First, the presenceof a TGOI with controlled expression properties that can be reproducedfor any GOI of the same class following CLD enables evaluation oftargeted changes to be performed in conditions that are predictive ofthe intended final use. Secondly, the continuous presence of anexpression load during the engineering workflow reduces the risk of lossof functionality due to genetic instability. As an added featuredirected evolution, screening of natural genetic diversity and targetedchanges can be combined in any form together with conditions predictableto the final use to generate the final improved host cell line. In oneembodiment of the invention the instability of the host cell genome isfirst used to enable generation of an improved host cell via multiplegenetic and/or epigenetic changes throughout the genome that wouldlikely be difficult to generate using targeted engineering alone. In asecond stage the instability of the genome is reduced either viadirected evolution/selection or via targeted engineering. Research iscurrently underway to define engineering targets enabling stabilizationof the genome of for example CHO cells [8].

As previously described the isolation/selection steps can also berepeated multiple times using a gradually increased expression load asoutlined in FIG. 2 . The rationale for a stepwise increase in theexpression load is to enable a gradual move towards a higher performancephenotype. If the initial expression load is too high a low number ofclones will be capable of matching this expression load and show up ascompetent producers during screening and hence a low number of clonescan be passed on to a second round of growth and screening. This leadsto an early potentially detrimental reduction of phenotypic diversity.There is a high risk for a low survival frequency and very low growth ofcultured cells again leading to an inefficient sampling of clonalvariation and slow accumulation of improved phenotypes. The initialclonal variation might not even be sufficient to enable survival of anycells at all. By gradually increasing the expression load cells cangradually adapt and an increased genetic variation can be sampled andtaken forward in each iteration.

The use of a host cell line based on an improved cell generated usingany of the above workflows together with expression vectors forSite-Directed Integration (SDI) enables a highly streamlined CLDworkflow. Current methods known in the art are generally based on eitherrandom integration of expression constructs or targeted integration ofexpression constructs into a genomic location having a SM region only.Using the random integration approach a pool of cells that are allactively transcribing genes in the expression construct can be generatedvia the aid of a selection marker. However, different clones will havethe expression construct integrated at different genomic locations andwith different number of copies. This in turn will result in a range oftranscription levels and importantly different clones will also displayvarying stability of transcription over time and during differentculture conditions. In addition different clones will display differentprotein production traits. In summary this leads to a need of massivescreening efforts to isolate a clone with both good transcription levelsand good protein production traits.

Furthermore, repeating the CLD using either an identical expressionconstruct or a variant expression construct will lead to cells that aredifferent at the genetic and phenotypic level making it difficult toevaluate optimal expression construct and GOI designs. Using a targetedapproach simplifies the workflow by the introduction of a single copy ofthe expression construct into a pre-defined/pre-characterized genomiclocation. The delivery of the expression construct to the definedlocation is aided by the presence of specific sequences at the genomiclocation and in the expression constructs and via the co-transfection ofa vector coding for a nucleic acid enzyme. The enzyme can either be anuclease introducing a double strand break unique to the genomiclocation and integration proceeds via homologous recombination between along stretch of homologous sequences present at the genomic site and inthe expression construct. As an alternative, shorter specific nucleotidesequences acting as target sequences for recombinases can be present atthe genomic location and in the expression construct. The co-transfectedrecombinase will then catalyze the integration of the expressionconstruct. After utilizing selection via a second SM set a pool of cellsall carrying a single copy of the expression construct and displayingsimilar transcription levels can be generated. However, different cloneswill still display different protein production traits and hence thereis a need for a clone screening procedure to isolate a cell with thedesired traits. Although the screening should be reduced as compared torandom integration it could still be a significant effort and cells canstill be different between different CLD efforts.

However, using the host cell line and the CLD methodology of the presentinvention potentially removes both of the above sources for variationand screening need and can potentially generate production clones/poolswith superior production traits as compared to current screening basedmethods. An improved host cell generated according to any combination ofthe approaches described above already displays the desired proteinproduction traits and has a Landing Pad region containing sequencesenabling targeted insertion of a desired gene of interest at the desiredgenomic location previously used to express the TGOI. This can beperformed in different ways as described in general terms above and indetail later but all workflows generally use some sort of selectionmarker. After selecting for proper insertion of the GOI a pool of cellswith limited diversity is generated. In principle, a clone from thispool could be isolated without further screening and only characterizedto ensure that a single correct GOI construct has been inserted and noadditional random integration.

Some examples of improvements over standard workflows have beendescribed in previous art. First, directed evolution of a final hostcell line has been proposed [9]. However, in this case directedevolution is performed on an initial cell line lacking the introductionof recombinant genes or a hot spot integration site and selection traitsare not directly linked to protein production traits. Further, thegenerated host cell line is then utilizing random integration for CLD.Host cells generated using this approach will not have been subjected toa pressure to accumulate changes improving protein production traits andas adaptation to specific culture conditions has been done without therecombinant expression burden there is a risk for sub-optimal adaptationto the conditions experienced during production of a recombinantprotein.

The present invention represents several improvements over thisapproach. The presence of the TGOI enables selection/evolution ofprotein production traits matching the combined demands of the specificculture conditions and a high level recombinant expression pressure.Further, the continuous presence of the TGOI reduces the risk for lossof adaptation due to genetic instability. Finally, the cassette exchangeapproach to CLD enables the conditions experienced by the cellsfollowing introduction of the GOI (at the same location, with the samecopy number and with the same sequence elements) to be highly similar tothe conditions used during generation of the host cell line. Utilizationof pre-adapted cells has also been proposed for targeted integrationbased CLD [10]. In this approach it is proposed that a cell linegenerated using random integration CLD and displaying desired proteinproduction traits should be selected as a source for generating a finalhost cell line. In the proposed procedure, the genomic location isidentified (must be a single site) and the recombinant constructs arecut out using gene editing based homologous recombination and exchangedfor a construct carrying a selection marker flanked by recombinasesequences.

After isolation of cells having undergone correct exchange, the genomicsite is treated with a recombinase to cut out the selection marker andleave a single recombinase site flanked by a promoter. This host cellline can then be used for targeted integration of a second expressionconstruct. In this approach there is not a match between the expressionload provided by the multiple copies of the first expression constructand the single copy of a second expression construct following CLD.Hence, the properties of the host cell line are not likely to be fullysuitable to the new conditions. This mismatch can be further increasedif the culture conditions are different between the initial cell lineand the second cell line. In addition, after the exchange of theoriginal expression construct there are multiple culture periods duringboth the construction of the host cell line and each CLD effort wherethe lack of recombinant expression load can lead to loss of accumulatedtraits and increased diversity of cells due to genetic instability.Hence, the current invention offers multiple improvements over thisapproach in that the selection/evolution of traits can be better matchedbetween host cell line and the cell line producing the GOI after CLD. Inaddition the presence of the TGOI or the GOI at a similar expressionload throughout all culture steps minimize the risk of loss offunctionality/increased cell diversity due to genetic instability. Inaddition the increased sampling of diversity possible by directedevolution and the possibility to add targeted modifications has thepotential to generate production clones with superior protein productiontraits.

Using the natural diversity of cells has recently been discussed andhighlighted as a potentially superior approach in a GEN article [13].Using selection to generate a high performance cell expressing a certaintemplate protein is here contemplated. However instead of isolating thiscell and using it directly in subsequent CLD workflows the potential toidentify engineering targets by detailed omics characterization toenable reproduction of a high productivity cellular phenotype usingtargeting engineering approaches is proposed.

Following the detailed outline of the general concept of the inventionand its benefits above specific implementations will now be described.In a first specific implementation the improved cell C2 (Cn+1) carryinga receiving DNA construct R is generated according to FIG. 3 or FIG. 4using a recombinase (Rec-RS2) to excise a TGOI region being flanked byreversible recombinase target sequences RS2. CLD using these improvedcells are outlined in FIG. 5 . The cell C2 containing one irreversiblerecombinase recognition sequence (RS1) and one reversible recombinaserecognition sequence (RS2) is contacted with a recombinase withspecificity for RS1/RS1′ and a matching Expression Vector (EV)containing a recombinant DNA construct R′ with a matching irreversiblerecombinase recognition sequence RS1′ a desired gene of interest (GOI)and a selection marker (SM2). Following insertion a cell or a pool ofcells having undergone correct modification is selected using theselection marker (SM2). The recombinases used can be of any reversibleand irreversible type such as attP/attB/PhiC31 as an irreversible systemand loxP/Cre as an reversible system.

In a second set of specific implementations, the template recombinantDNA construct T of the improved cell C1 is modified to a receivingrecombinant DNA construct R (generating the cell C2) via the use of geneediting approaches as outlined in FIG. 7 . The improved cell C1 containstwo long sequences (>300 bp and typically >=1 Kb) X and Y flanking thetemplate gene of interest and an optional selection marker and beingunique or rare in the genome G1. Further the flanked region contains anadditional shorter sequence z (15-40 nt) being unique or rare in thegenome G1. As C1 is contacted with a donor vector (DV) containing arecombinant DNA construct T′ and a site specific gene editing DNAnuclease with specificity for z (Nz) a cassette exchange between T andT′ occurs via homologous repair mechanisms catalyzed by a double strandbreak at z. The two sequences X′ and Y′ are identical or highlyhomologous to the sequences X and Y in the genome G1. The resultingrecombinant DNA construct R contains sequences Q enabling targetedintegration of a GOI into the hot spot region HS. The site specificnuclease can be based on any gene editing solution such as zinc fingernucleases, homing endonucleases, TALENs or CRISPR/Cas9 variants or otherCRISPR systems.

One approach utilizes a receiving DNA construct design R in which anoptional SM gene(s) are flanked by two recombinase recognition sequences(RS) and an expression vector design in which a GOI(s) and an optionalsecond SM gene(s) are flanked by matching recombinase recognitionsequences (RS′). By co-transfecting the improved cell C1 with theexpression vector in the form of a plasmid and a plasmid encoding arecombinase (Rec-RS) with specificity for RS/RS' a cassette exchangebetween R and R′ is achieved. A cell C3 having undergone the correctexchange only can be selected via the difference in SMs between R andR′. The resulting recombinant DNA construct E contains recombinedrecombinase recognition sequences RC. Depending on the recombinasesystem used these can either be different from RS and RS' and differbetween the 5′ and 3′ sequences (as for attP/attB/PhiC31) or beidentical to RS/RS' (as for loxP/Cre). The recombinase recognitionsequences used can be of any type such as a serine recombinase type suchas attP/attB or a tyrosine recombinase type such as Lox, Rox or FRTtogether with matching recombinases such as PhiC31, Cre, Dre, or Flp.Different examples of this approach based on varying the promoterplacement for R and R′ are outlined in FIG. 8 .

In another approach the receiving DNA construct R contains a singlerecombinase recognition sequence RS followed by an optional SM gene(s)and the matching expression vector EV a single matching recombinaserecognition sequence RS' followed by a GOI(s) and a SM gene(s) in anyorder. By co-transfecting the improved cell C1 with the expressionvector in the form of a plasmid and a plasmid encoding a recombinase(Rec-RS) with specificity for RS/RS′ the R′ construct is introduced intothe cell and simultaneously changing the relative position of theoriginal R construct so that the resulting E recombinant DNA constructis a combination of R and R′. Different examples of this approach basedon varying the promoter placement for R and R′ are outlined in FIG. 9 .

In any of the above embodiments of the invention the TGOI/GOI couldcontain a single gene of interest coding for proteins such as growthfactors, blood clotting factors, cytokines, hormones, erythropoietins,albumins, virus proteins, virus protein mimics, bacterial proteins,bacterial protein mimics, domain antibodies, ScFvs, Affibodies, DARPINs,multimerization domains, IgG Fc domains, albumin binding domains, Fcreceptor binding domains or fusion proteins based on combinations of theabove single gene of interest coded protein classes. The TGOI/GOI couldalso contain two or more genes of interest coding for proteins such asmonoclonal antibodies based on naturally occurring scaffolds,bi-specific antibodies based on naturally occurring scaffolds, Fabs,virus like particles, multiple chain proteins based on association oftwo or more different protein chains selected from the list of singlegene coded proteins above. In preferred embodiments of the invention theTGOI of the host cell line and the GOI used for CLD encode proteinsbelonging to the same protein class. In further preferred embodimentsthe TGOI is a hard to express protein of that protein class.

In further preferred embodiments a single copy of TGOI and GOI is used.In further preferred embodiments genetic elements, such as promoter(s),5′-UTR(s), signal peptide(s), design principle for synonymous nucleotideencoding in the coding region and 3′-UTR(s), used in the TGOI and GOIare identical. In some embodiments multiple final host cell linescontaining different TGOIs of the same protein class but with differentamino acid ratios are available and the specific cell line used for CLDusing a specific GOI is selected based on closest match between aminoacid ratios of the template protein of interest (encoded by TGOI) andthe desired protein of interest (encoded by GOI). In some embodimentsmultiple final host cell lines containing identical TGOIs butselected/derived to display a specific protein quality profile, such asa specific glycoprofile, are available. The specific cell line used forCLD using a specific GOI is selected based on closest match betweendesired protein quality profile and available protein quality profiles.

REFERENCES

-   [1] Hacker, D. L., De Jesus, M., Wurm, F. M., 2009. 25 years of    recombinant proteins from reactor-grown cells—where do we go from    here? Biotechnology Advances 27, 1023-1027.-   [2] Wirth, D., et al., Road to precision: recombinase-based    targeting technology for genome engineering. Current Opinion in    Biotechnology, 2007.-   [3] D. Wirth, L. Gama-Norton, R. Schucht, K. Nehlsen “Site-Directed    Engineering of Defined Chromosomal Sites for Recombinant Protein and    Virus Expression-Site-directed engineering of defined chromosomal    sites”, BioPharm International, Volume 22, Issue 7 (2009)-   [4] Alexandra Baer and Jürgen Bode, Coping with kinetic and    thermodynamic barriers: RMCE, an efficient strategy for the targeted    integration of transgenes, Current Opinion in Biotechnology 2001,    12:473-480-   [5] Wei-shou Hu; Cell Culture Bioprocessing Engineering; ISBN    978-0-9856626-0-8, pages 127-146-   [6] WO2009/075886 (Translation Enhancer Elements, TEEs)-   [7] WO2010/98861 (RESCUE)-   [8]    http://www.chorus.co.at/projects/genomic-stability-of-the-host-cell-line.html,    Dec. 3, 2014-   [9] Nazanin Dadehbeigi et al.; Robust and efficient recombinant mAb    production using a proprietary CHO host cell with improved    characteristics identified through directed evolution, conference    poster    http://www.fujifilmdiosynth.com/pdfs/CCE_XIV_Poster_Fay_Saunders.pdf-   [10] Eric Rhodes; Gene editing approaches for viable commercial    production; conference presentation Bioprocess summit Boston August    2012-   [11] U.S. Pat. No. 6,632,672 (Stanford att-site patent).-   [12] A Brown et al.; Synthetic promoters for CHO cell engineering;    Biotechnology and Bioengineering vol 111(8) 1638-1647 (2014).-   [13] Angelo DePalma; Cell-Line Optimization: Nature or Nurture? Are    Great Cell Lines Born or Made? Both!; GEN Nov. 1, 2015 (Vol. 35, No.    19)

1. A method to obtain a cell suitable for expressing a protein interestcomprising the following steps: a) integration of a nucleic acidmolecule encoding a first protein of interest into a pre-defined site inthe genome of a recipient cell; b) identification of cells expressingthe first protein of interest; c) excision of the nucleic acid moleculeencoding the first protein of interest from the genome of the identifiedcells and simultaneously introducing one or several functional sequenceelements Q enabling targeted introduction of a nucleic acid moleculeencoding a second protein of interest into said pre-defined site in thegenome, wherein the genome of the recipient cell does not comprise theone or several sequence elements Q prior to excision of the nucleic acidmolecule encoding the first protein of interest; and d) subsequent tostep c), integration of the nucleic acid molecule encoding the secondprotein of interest into the pre-defined site in the genome of theresulting cell.
 2. The method according to claim 1, further comprisingcreating of a cell line suitable for production of said second proteinof interest as a recombinant protein.
 3. The method according to claim2, wherein the recombinant protein is an active pharmacologicalingredient.
 4. The method according to claim 2, further comprising herecombinant protein as an ingredient in a diagnostic reagent.
 5. Themethod according to claim 2, further comprising providing therecombinant protein as a reagent in an industrial process.
 6. The methodaccording to claim 1, wherein the first protein of interest is afluorescent protein.
 7. The method according to claim 1, wherein thefirst protein of interest is an immunoglobulin or immunoglobulin-likeprotein.
 8. The method according to claim 1, further comprisingselecting a cell with increased capacity to express the first protein ofinterest relative to other cells identified as expressing the firstprotein of interest prior to excision of the nucleic acid moleculeencoding the first protein of interest.
 9. The method according to claim8, wherein selecting the cell with increased capacity to express thefirst protein of interest comprises isolating clones from a culture ofsaid identified cells expressing the first protein of interest.
 10. Themethod according to claim 8, wherein selecting the cell with increasedcapacity to express the first protein of interest comprises isolatingpools or clones from said identified cells expressing the first proteinof interest after (1) different culture time in a continuous cultureformat such as a perfusion culture or (2) different number of individualcultures starting with inoculation of a first culture using saididentified cells expressing the first protein of interest and using avolume from a finished culture to inoculate a next culture or (3) acombination of (1) and (2).
 11. The method according to claim 8, whereinselecting the cell with increased capacity to express the first proteinof interest comprises performing targeted engineering by applying geneediting methods to introduce, remove or modify genetic material in thegenome of said identified cells expressing the first protein ofinterest.
 12. The method according to claim 1, wherein a selectionmarker is simultaneously introduced with the one or several functionalsequence elements Q.
 13. The method according to claim 1, wherein thenucleic acid molecule encoding the first protein of interest, whenintegrated into the recipient cell, comprises flanking sequences X and Yflanking the nucleic acid molecule encoding the first protein ofinterest, wherein the flanked region comprises a sequence z being uniqueor rare in the genome, and step c) comprises forming a double strandbreak with a specific gene editing DNA nuclease at sequence z andperforming a cassette exchange with a template DNA construct containingthe one or several functional sequence elements Q.
 14. The methodaccording to claim 1, wherein the one or several functional sequenceelements Q comprises one or more recombinase recognition sequences. 15.The method according to claim 1, wherein the first protein of interestand the second protein of interest are of the same protein class. 16.The method according to claim 1, wherein only a single copy of thenucleic acid molecule encoding the first protein of interest and/or thenucleic acid molecule encoding the second protein of interest isintegrated.